It only works in Chrome, which is a pretty big issue.
Per wikipedia [0], other browsers rejected PNaCL because they don't like the idea of web apps running binaries as that represents a black box for most users. In comparison, wasm is "more open". Wasm code has a human-readable text equivalent (although, frankly, the number of people who will be able to make sense of it is not high and doesn't include me).
[0] https://en.wikipedia.org/wiki/Google_Native_Client#Detractor...